1
|
Sinha P, Yadav AK. Repurposing integrase inhibitors against human T-lymphotropic virus type-1: a computational approach. J Biomol Struct Dyn 2024:1-12. [PMID: 38234060 DOI: 10.1080/07391102.2024.2304681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Adult T-cell Lymphoma (ATL) is caused by the delta retrovirus family member known as Human T-cell Leukaemia Type I (HTLV-1). Due to the unavailability of any cure, the study gained motivation to identify some repurposed drugs against the virus. A quick and accurate method of screening licensed medications for finding a treatment for HTLV-1 is by cheminformatics drug repurposing in order to analyze a dataset of FDA approved integrase antivirals against HTLV-1 infection. To determine how the antiviral medications interacted with the important residues in the HTLV-1 integrase active regions, molecular docking modeling was used. The steady behavior of the ligands inside the active region was then confirmed by molecular dynamics for the probable receptor-drug complexes. Cabotegravir, Raltegravir and Elvitegravir had the best docking scores with the target, indicating that they can tightly bind to the HTLV-1 integrase. Moreover, MD simulation revealed that the Cabotegravir-HTLV-1, Raltegravir-HTLV-1 and Elvitegravir-HTLV-1 interactions were stable. It is obvious that more testing of these medicines in both clinical trials and experimental tests is necessary to demonstrate their efficacy against HTLV-1 infection.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Prashasti Sinha
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Anil Kumar Yadav
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| |
Collapse
|
2
|
Misra R, Vijayakanth T, Shimon LJW, Adler-Abramovich L. Atomic insight into short helical peptide comprised of consecutive multiple aromatic residues. Chem Commun (Camb) 2022; 58:6445-6448. [PMID: 35548938 DOI: 10.1039/d2cc01038k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The occurrence of sequential multiple aromatic residues in a helical sequence is rare compared to the β-sheet rich structure. Here, using helix promoting α-aminoisobutyric acid (Aib) residues, we unravel atomistic details of the helical secondary structure formation and the super helical assembly of two heptapeptides composed of sequential five and six phenylalanine (Phe) residues.
Collapse
Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Physics & Chemistry of Living Systems, and the Center for Nanoscience and Nanotechnology, Tel-Aviv University, 69978, Israel. .,Dept. of Med. Chem, NIPER Mohali, S.A.S. Nagar, Mohali, 160062, India
| | - Thangavel Vijayakanth
- The Shmunis School of Biomedicine and Cancer Research George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 761000, Rehovot, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Physics & Chemistry of Living Systems, and the Center for Nanoscience and Nanotechnology, Tel-Aviv University, 69978, Israel.
| |
Collapse
|
3
|
Garcia Garcia C, Patkar SS, Jovic N, Mittal J, Kiick KL. Alteration of Microstructure in Biopolymeric Hydrogels via Compositional Modification of Resilin-Like Polypeptides. ACS Biomater Sci Eng 2021; 7:4244-4257. [DOI: 10.1021/acsbiomaterials.0c01543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Cristobal Garcia Garcia
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Sai S. Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Delaware Biotechnology Institute, Newark, Delaware 19716, United States
- Biomedical Engineering, University of Delaware, Newark, Delaware 19176, United States
| |
Collapse
|
4
|
Zhang J, Liu S, Li H, Tian X, Li X. Tryptophan-Based Self-Assembling Peptides with Bacterial Flocculation and Antimicrobial Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11316-11323. [PMID: 32907333 DOI: 10.1021/acs.langmuir.0c01957] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tryptophan as an aromatic amino acid with a hydrophobic indole group plays important roles in stabilizing protein structures and enhancing molecular bindings in nature, but was rarely used in the molecular design of self-assembling peptides or gelators. Therefore, we prepared a series of short peptides from Trp amino acids and examined the potential roles of Trp residues for regulating peptide self-assembly and gelation. The introduced Trp amino acids not only diversify the molecular structures of peptide gelators, but also promote aromatic and hydrogen-bonding interactions for supramolecular self-assembling and gelation, which generates self-assembled nanostructures with twisted helical morphologies and supramolecular hydrogels with low minimal gelation concentrations. More importantly, the self-assembling peptides with Trp residues displayed strong preference for interacting with the lipidic membranes of bacteria, which resulted in bacterial flocculation and the death of E. coli and S. aureus.
Collapse
Affiliation(s)
- Jikun Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Shengnan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Hang Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xin Tian
- School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Xinming Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| |
Collapse
|
5
|
Guzmán F, Wong G, Román T, Cárdenas C, Alvárez C, Schmitt P, Albericio F, Rojas V. Identification of Antimicrobial Peptides from the Microalgae Tetraselmis suecica (Kylin) Butcher and Bactericidal Activity Improvement. Mar Drugs 2019; 17:md17080453. [PMID: 31374937 PMCID: PMC6722934 DOI: 10.3390/md17080453] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 11/16/2022] Open
Abstract
The outburst of microbial resistance to antibiotics creates the need for new sources of active compounds for the treatment of pathogenic microorganisms. Marine microalgae are of particular interest in this context because they have developed tolerance and defense strategies to resist the exposure to pathogenic bacteria, viruses, and fungi in the aquatic environment. Although antimicrobial activities have been reported for some microalgae, natural algal bioactive peptides have not been described yet. In this work, acid extracts from the microalga Tetraselmis suecica with antibacterial activity were analyzed, and de novo sequences of peptides were determined. Synthetic peptides and their alanine and lysine analogs allowed identifying key residues and increasing their antibacterial activity. Additionally, it was determined that the localization of positive charges within the peptide sequence influences the secondary structure with tendency to form an alpha helical structure.
Collapse
Affiliation(s)
- Fanny Guzmán
- Nucleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Genezareth Wong
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Tanya Román
- Nucleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Constanza Cárdenas
- Nucleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Claudio Alvárez
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo 1781421, Chile
- Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo 1781421, Chile
| | - Paulina Schmitt
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Fernando Albericio
- Department of Organic Chemistry and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain
- School of Chemistry, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| |
Collapse
|
6
|
Basuyaux G, Desmarchelier A, Gontard G, Vanthuyne N, Moussa J, Amouri H, Raynal M, Bouteiller L. Extra hydrogen bonding interactions by peripheral indole groups stabilize benzene-1,3,5-tricarboxamide helical assemblies. Chem Commun (Camb) 2019; 55:8548-8551. [PMID: 31268082 DOI: 10.1039/c9cc03906f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Benzene-1,3,5-tricarboxamide monomers derived from alkyl esters of tryptophan (BTA Trp) self-assemble into helices with an inner threefold hydrogen bond network surrounded by a second network involving the indole N-H groups. As a consequence of this extra stabilization of its helical assemblies, BTA Trp forms more viscous solutions than a range of ester and alkyl BTAs.
Collapse
Affiliation(s)
- Gaëtan Basuyaux
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| | - Alaric Desmarchelier
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| | - Geoffrey Gontard
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| | - Nicolas Vanthuyne
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2, UMR 7313, 13397 Marseille Cedex 20, France
| | - Jamal Moussa
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| | - Hani Amouri
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| | - Matthieu Raynal
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| | - Laurent Bouteiller
- Sorbonne Université CNRS, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, 75005 Paris, France.
| |
Collapse
|
7
|
Abstract
Water has a profound effect on the dynamics of biomolecules and governs many biological processes, leading to the concept that function is slaved to solvent dynamics within and surrounding the biomolecule. Protein conformational changes on μs-ms time scales are frequently associated with protein function, but little is known about the behavior of protein-bound water on these time scales. Here we have used NMR relaxation dispersion measurements to probe the tryptophan indoles in the enzyme dihydrofolate reductase (DHFR). We find that during structural changes on the μs-ms time scale, large chemical shift changes are often observed for the NH proton on the indole ring, while relatively smaller chemical shift changes are observed for the ring nitrogen atom. Comparison with experimental chemical shifts and density functional theory-based chemical shift predictions show that during the structural change the tryptophan indole NHs remain bound to water, but the geometry of the protein-bound water networks changes. These results establish that relaxation dispersion measurements can indirectly probe water dynamics and indicate that water can influence, or be influenced by, protein conformational changes on the μs-ms time scale. Our data show that structurally conserved bound water molecules can play a critical role in transmitting information between functionally important regions of the protein and provide evidence that internal protein motions can be coupled through the mediation of hydrogen-bonded water bound in the protein structure.
Collapse
Affiliation(s)
- R. Bryn Fenwick
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| | - David Oyen
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| | - H. Jane Dyson
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| | - Peter E. Wright
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| |
Collapse
|
8
|
Makwana KM, Mahalakshmi R. Capping β-hairpin with N-terminal d-amino acid stabilizes peptide scaffold. Biopolymers 2017; 106:260-6. [PMID: 26999275 DOI: 10.1002/bip.22837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022]
Abstract
Various strategies exist to stabilize de novo designed synthetic peptide β-hairpins or β-sheets structures, especially at the non-hydrogen bonding position. However, strategies to stabilize strand termini, which are affected by fraying, are highly limited. Here, by substituting N-terminal aliphatic amino acid with its mirror image counterpart, we achieve a significant increase in scaffold stabilization, resulting from the formation of a terminal aliphatic-aromatic hydrophobic CH…pi cluster. Our extensive solution NMR studies support the incorporation of an N-terminal d-aliphatic amino acid in the design of short β-hairpins, while successfully retaining the overall structural scaffold. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 260-266, 2016.
Collapse
Affiliation(s)
- Kamlesh M Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, Madhya Pradesh, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, Madhya Pradesh, India
| |
Collapse
|
9
|
Romero-Romero S, Gomez Lagunas F, Balleza D. Side chain flexibility and coupling between the S4-S5 linker and the TRP domain in thermo-sensitive TRP channels: Insights from protein modeling. Proteins 2017; 85:630-646. [PMID: 28066924 DOI: 10.1002/prot.25243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 11/11/2022]
Abstract
The transient receptor potential (TRP) superfamily is subdivided into several subfamilies on the basis of sequence similarity, which is highly heterogeneous but shows a molecular architecture that resembles the one present in members of the Kv channel superfamily. Because of this diversity, they produce a large variety of channels with different gating and permeability properties. Elucidation of these particular features necessarily requires comparative studies based on structural and functional data. The present study aims to compilate, analyze, and determine, in a coherent way, the relationship between intrinsic side-chain flexibility and the allosteric coupling in members of the TRPV, TRPM, and TRPC families. Based on the recently determined structures of TRPV1 and TRPV2, we have generated protein models for single subunits of TRPV5, TRPM8, and TRPC5 channels. With these models, we focused our attention on the apparently crucial role of the GP dipeptide at the center of the S4-S5 linker and discussed its role in the interaction with the TRP domain, specifically with the highly-conserved Trp during this coupling. Our analysis suggests an important role of the S4-S5L flexibility in the thermosensitivity, where heat-activated channels possess rigid S4-S5 linkers, whereas cold-activated channels have flexible ones. Finally, we also present evidence of the key interaction between the conserved Trp residue of the TRP box and of several residues in the S4-S5L, importantly the central Pro. Proteins 2017; 85:630-646. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sergio Romero-Romero
- Facultad de Medicina, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Mexico city, MEXICO
| | - Froylan Gomez Lagunas
- Facultad de Medicina, Departamento de Fisiología, Universidad Nacional Autónoma de México, Mexico city, MEXICO
| | - Daniel Balleza
- Facultad de Medicina, Departamento de Fisiología, Universidad Nacional Autónoma de México, Mexico city, MEXICO
| |
Collapse
|
10
|
Voda AS, Magniez K, Salim NV, Wong C, Guo Q. Synthesis and self-assembly behaviour of poly(Nα-Boc- l-tryptophan)-block-poly(ethylene glycol)-block-poly(Nα-Boc- l-tryptophan). RSC Adv 2016. [DOI: 10.1039/c6ra03718f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report for the first time the use of Nα-Boc-l-tryptophan for the synthesis of amphiphilic BAB triblock copolymers for potential drug delivery applications.
Collapse
Affiliation(s)
- Andreea S. Voda
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Kevin Magniez
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Nisa V. Salim
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Cynthia Wong
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Qipeng Guo
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| |
Collapse
|
11
|
Madhusudan Makwana K, Mahalakshmi R. Implications of aromatic-aromatic interactions: From protein structures to peptide models. Protein Sci 2015; 24:1920-33. [PMID: 26402741 DOI: 10.1002/pro.2814] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022]
Abstract
With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.
Collapse
Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
| |
Collapse
|
12
|
Meyer D, Mutschler C, Robertson I, Batt A, Tatko C. Aromatic interactions with naphthylalanine in a β
-hairpin peptide. J Pept Sci 2013; 19:277-82. [DOI: 10.1002/psc.2496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Meyer
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Caleb Mutschler
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Ian Robertson
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Alexandra Batt
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Chad Tatko
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| |
Collapse
|
13
|
Abstract
The transmembrane domains (TMDs) of integral membrane proteins do not merely function as membrane anchors but play active roles in many important biological processes. The downregulation of the CD4 coreceptor by the Vpu protein of HIV-1 is a prime example of a process that is dependent on specific properties of TMDs. Here we report the identification of Trp22 in the Vpu TMD and Gly415 in the CD4 TMD as critical determinants of Vpu-induced targeting of CD4 to endoplasmic reticulum (ER)-associated degradation (ERAD). The two residues participate in different aspects of ERAD targeting. Vpu Trp22 is required to prevent assembly of Vpu into an inactive, oligomeric form and to promote CD4 polyubiquitination and subsequent recruitment of the VCP-UFD1L-NPL4 dislocase complex. In the presence of a Vpu Trp22 mutant, CD4 remains integrally associated with the ER membrane, suggesting that dislocation from the ER into the cytosol is impaired. CD4 Gly415, on the other hand, contributes to CD4-Vpu interactions. We also identify two residues, Val20 and Ser23, in the Vpu TMD that mediate retention of Vpu and, by extension, CD4 in the ER. These findings highlight the exploitation of several TMD-mediated mechanisms by HIV-1 Vpu in order to downregulate CD4 and thus promote viral pathogenesis.
Collapse
|
14
|
Santiveri CM, Jiménez MA. Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides. Biopolymers 2011; 94:779-90. [PMID: 20564027 DOI: 10.1002/bip.21436] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials.
Collapse
Affiliation(s)
- Clara M Santiveri
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, Madrid 28006, Spain
| | | |
Collapse
|
15
|
Purohit P, Auerbach A. Energetics of gating at the apo-acetylcholine receptor transmitter binding site. ACTA ACUST UNITED AC 2010; 135:321-31. [PMID: 20351060 PMCID: PMC2847916 DOI: 10.1085/jgp.200910384] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acetylcholine receptor channels switch between conformations that have a low versus high affinity for the transmitter and conductance for ions (R↔R*; gating). The forward isomerization, which begins at the transmitter binding sites and propagates ∼50 Å to the narrow region of the pore, occurs by approximately the same sequence of molecular events with or without agonists present at the binding sites. To pinpoint the forces that govern the R versus R* agonist affinity ratio, we measured single-channel activation parameters for apo-receptors having combinations of mutations of 10 transmitter binding site residues in the α (Y93, G147, W149, G153, Y190, C192, and Y198), ε (W55 and P121), or δ (W57) subunit. Gating energy changes were largest for the tryptophan residues. The αW149 energy changes were coupled with those of the other aromatic amino acids. Mutating the aromatic residues to Phe reduces the R/R* equilibrium dissociation constant ratio, with αY190 and αW149 being the most sensitive positions. Most of the mutations eliminated long-lived spontaneous openings. The results provide a foundation for understanding how ligands trigger protein conformational change.
Collapse
Affiliation(s)
- Prasad Purohit
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | | |
Collapse
|
16
|
Csontos J, Murphy RF, Lovas S. The role of weakly polar and H-bonding interactions in the stabilization of the conformers of FGG, WGG, and YGG: an aqueous phase computational study. Biopolymers 2008; 89:1002-11. [PMID: 18615659 DOI: 10.1002/bip.21049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The energetics of intramolecular interactions on the conformational potential energy surface of the terminally protected N-Ac-Phe-Gly-Gly-NHMe (FGG), N-Ac-Trp-Gly-Gly-NHMe (WGG), and N-Ac-Tyr-Gly-Gly-NHMe (YGG) tripeptides was investigated. To identify the representative conformations, simulated annealing molecular dynamics (MD) and density functional theory (DFT) methods were used. The interaction energies were calculated at the BHandHLYP/aug-cc-pVTZ level of theory. In the global minima, 10%, 31%, and 10% of the stabilization energy come from weakly polar interactions, respectively, in FGG, WGG, and YGG. In the prominent cases 46%, 62%, and 46% of the stabilization energy is from the weakly polar interactions, respectively, in FGG, WGG, and YGG. On average, weakly polar interactions account for 15%, 34%, and 9% of the stabilization energies of the FGG, WGG, and YGG conformers, respectively. Thus, weakly polar interactions can make an important energetic contribution to protein structure and function.
Collapse
Affiliation(s)
- József Csontos
- Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, NE 68178, USA
| | | | | |
Collapse
|
17
|
Liu H, Lu S, Xu J, Du D. Asymmetric Friedel–Crafts Alkylation of Electron‐Rich N‐Heterocycles with Nitroalkenes Catalyzed by Diphenylamine‐Tethered Bis(oxazoline) and Bis(thiazoline) ZnIIComplexes. Chem Asian J 2008; 3:1111-21. [DOI: 10.1002/asia.200800071] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
18
|
Csontos J, Palermo NY, Murphy RF, Lovas S. Calculation of weakly polar interaction energies in polypeptides using density functional and local Møller-Plesset perturbation theory. J Comput Chem 2008; 29:1344-52. [PMID: 18172837 DOI: 10.1002/jcc.20898] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The interaction energies of ubiquitous weakly polar interactions in proteins are comparable with those of hydrogen bonds, consequently, they stabilize local, secondary, and tertiary structures. However, the most widely-used density functionals fail to describe the weakly polar interactions. Thus, it is important to find and test functionals which adequately describe and quantify the energetics of such interactions. For this purpose, interaction energies in the hydrophobic core of rubredoxin (PDB id: 1rb9) and in the S22 subset of the JSCH-2005 benchmark database were computed with the BHandHLYP and PWPW91 functionals and with the pseudospectral implementation of the local MP2 (PS-LMP2) method. The cc-pVDZ, cc-pVTZ(-f), cc-pVTZ, cc-pVQZ(-g), aug-cc-pVDZ, aug-cc-VTZ(-f), and aug-cc-pVTZ basis sets were used for the calculations. In the S22 subset the PS-LMP2 results were extrapolated to the complete basis set limit. Furthermore, the a posteriori counterpoise method of Boys and Bernardi was used to correct the basis set superposition errors in the calculation of interaction energies. Calculations using the BHandHLYP functional, both for the various weakly polar interactions in rubredoxin and for the dispersion interactions in the S22 subset, were in good agreement with those using the coupled cluster (CCSD(T)) and the resolution of identity MP2 (RIMP2) methods and clearly outperformed both the PWPW91 functional and the PS-LMP2 method. The results for the S22 hydrogen bonded subset, obtained with PWPW91 calculations, were closest to those of the reference high level calculations. For the "mixed" (hydrogen bonded and dispersive) interactions in the S22 subset, results obtained with the BHandHLYP and PS-LMP2 calculations agreed well with the reference calculations.
Collapse
Affiliation(s)
- József Csontos
- Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | | | | | | |
Collapse
|
19
|
Mahalakshmi R, Sengupta A, Raghothama S, Shamala N, Balaram P. Tryptophan rich peptides: influence of indole rings on backbone conformation. Biopolymers 2007; 88:36-54. [PMID: 17091496 DOI: 10.1002/bip.20625] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Synthetic peptides with defined secondary structure scaffolds, namely hairpins and helices, containing tryptophan residues, have been investigated in this study to probe the influence of a large number of aromatic amino acids on backbone conformations. Solution NMR investigations of Boc-W-L-W-(D)P-G-W-L-W-OMe (peptide 1), designed to form a well-folded hairpin, clearly indicates the influence of flanking aromatic residues at the (D)Pro-Gly region on both turn nucleation and strand propagation. Indole-pyrrolidine interactions in this peptide lead to the formation of the less-frequent type I' turn at the (D)Pro-Gly segment and frayed strand regions, with the strand residues adopting local helical conformations. An analog of peptide 1 with an Aib-Gly turn-nucleated hairpin (Boc-W-L-W-U-G-W-L-W-OMe (peptide 2)) shows a preference for helical structures in solution, in both chloroform and methanol. Peptides with either one (Boc-W-L-W-U-W-L-W-OMe (peptide 3)) or two (Boc-U-W-L-W-U-W-L-W-OMe (peptide 4)) helix-nucleating Aib residues give rise to the well-folded helical conformations in the chloroform solution. The results are indicative of a preference for helical folding in peptides containing a large number of Trp residues. Investigation of a tetrapeptide analog of peptide 2, Boc-W-U-G-W-OMe (peptide 5), in solution and in the crystal state (by X-ray diffraction), also indicates a preference for a helical fold. Additionally, peptide 5 is stabilized in crystals by both aromatic interactions and an array of weak interactions. Examination of Trp-rich sequences in protein structures, however, reveals no secondary structure preference, suggesting that other stabilizing interactions in a well-folded protein may offset the influence of indole rings on backbone conformations.
Collapse
|